Hi all,
I subsampled Illumina fastqs twice using 2 different random seeds. I then mapped all of the reads and got a total number of mapped reads and a mapped percent.
For the same sample, I am trying to select the higher map%, as I have found for the vast majority of my samples seqtk underestimates the actual map%.
The format of my tsv file is as follows:
sample1 200000 120000 60%
sample1 200000 115000 57.5%
sample2 200000 180000 90%
sample2 200000 190000 95%
...
sampleX 200000 180000 90%
sampleX 200000 182000 91%
I want to iterate over column 1 in the file, and select the line for data in column 3 or 4 (it doesn't matter) that is higher. So my example output from the above would be:
sample1 200000 120000 60%
sample2 200000 190000 95%
...
sampleX 200000 182000 91%
Looking forward to hearing your thoughts! Thanks
2 answers
Removing the % from $4, then sorting $4 in descending numeric order and choosing only unique IDs of $1 gives the intended output. The advantage of this over any if/else iterative script that checks the lines after the current one for other occurrences of the same $1 is that the input is not required to be sorted in any fashion:
awk '{gsub("%",""); print}' test.txt | sort -k4,4rn | sort -k1,1 -u | awk 'OFS="\t", $4 =$4"%" {print}'
with datamash. Added an extra row to check for sorting.
$ sed 's/%//g' test.txt | datamash -sfg 1 max 4| cut --complement -f5 | sed 's/$/%/g'
sample1 200000 120000 90%
sample2 200000 190000 95%
$ cat test.txt
sample1 200000 120000 60%
sample1 200000 115000 57.5%
sample2 200000 180000 90%
sample2 200000 190000 95%
sample1 200000 120000 90%
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